HEADER HYDROLASE 12-OCT-10 3P75 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS V104D TITLE 2 AT CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE; COMPND 5 EC: 3.1.31.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS STAPHYLOCOCCAL NUCLEASE, HYPERSTABLE VARIANT, PDTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.S.KHANGULOV,J.L.SCHLESSMAN,A.HEROUX,E.B.GARCIA-MORENO REVDAT 3 06-SEP-23 3P75 1 REMARK SEQADV LINK REVDAT 2 08-NOV-17 3P75 1 REMARK REVDAT 1 17-NOV-10 3P75 0 JRNL AUTH V.S.KHANGULOV,J.L.SCHLESSMAN,E.B.GARCIA-MORENO JRNL TITL CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT JRNL TITL 2 DELTA+PHS V104D AT CRYOGENIC TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 10782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 535 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 786 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1034 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.507 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1110 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1502 ; 1.023 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 137 ; 6.495 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 50 ;34.507 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 216 ;17.193 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 6.880 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 161 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 815 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 654 ; 1.433 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1052 ; 2.080 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 456 ; 3.871 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 445 ; 5.625 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 41 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1171 -1.9972 3.0153 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.1065 REMARK 3 T33: 0.0927 T12: -0.0107 REMARK 3 T13: -0.0003 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 3.3386 L22: 6.1702 REMARK 3 L33: 2.8642 L12: -1.6843 REMARK 3 L13: 0.0940 L23: 0.5803 REMARK 3 S TENSOR REMARK 3 S11: -0.0019 S12: 0.0823 S13: -0.2485 REMARK 3 S21: -0.1265 S22: 0.1958 S23: -0.0482 REMARK 3 S31: 0.2789 S32: 0.1167 S33: -0.1939 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 42 A 68 REMARK 3 ORIGIN FOR THE GROUP (A): 11.8547 6.0519 15.8312 REMARK 3 T TENSOR REMARK 3 T11: 0.2152 T22: 0.3393 REMARK 3 T33: 0.0885 T12: 0.0642 REMARK 3 T13: 0.0215 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 5.9973 L22: 9.8760 REMARK 3 L33: 4.6823 L12: 2.2050 REMARK 3 L13: 0.7692 L23: 0.8946 REMARK 3 S TENSOR REMARK 3 S11: 0.0460 S12: -0.9145 S13: 0.0431 REMARK 3 S21: 0.7907 S22: 0.1171 S23: 0.0196 REMARK 3 S31: 0.0123 S32: 0.1103 S33: -0.1631 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 69 A 103 REMARK 3 ORIGIN FOR THE GROUP (A): 8.4185 0.4259 1.1723 REMARK 3 T TENSOR REMARK 3 T11: 0.1152 T22: 0.0933 REMARK 3 T33: 0.0911 T12: -0.0323 REMARK 3 T13: -0.0305 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 5.1102 L22: 3.5573 REMARK 3 L33: 3.9708 L12: -0.4996 REMARK 3 L13: -0.4798 L23: 0.5289 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.3498 S13: -0.4000 REMARK 3 S21: -0.1230 S22: 0.1978 S23: 0.1670 REMARK 3 S31: 0.3342 S32: -0.2620 S33: -0.1491 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 104 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): 6.2629 12.4510 4.0081 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.0711 REMARK 3 T33: 0.1132 T12: -0.0062 REMARK 3 T13: 0.0054 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 4.8109 L22: 6.5950 REMARK 3 L33: 6.1023 L12: -1.0941 REMARK 3 L13: -0.6519 L23: -2.4825 REMARK 3 S TENSOR REMARK 3 S11: -0.1767 S12: 0.0357 S13: 0.3779 REMARK 3 S21: 0.0377 S22: 0.3200 S23: 0.2917 REMARK 3 S31: 0.0150 S32: -0.1708 S33: -0.1433 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 117 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3342 9.7270 -2.6068 REMARK 3 T TENSOR REMARK 3 T11: 0.0834 T22: 0.1627 REMARK 3 T33: 0.1235 T12: -0.0358 REMARK 3 T13: -0.0583 T23: 0.0813 REMARK 3 L TENSOR REMARK 3 L11: 8.3352 L22: 8.0196 REMARK 3 L33: 10.2969 L12: -5.0487 REMARK 3 L13: -6.9060 L23: 4.1995 REMARK 3 S TENSOR REMARK 3 S11: 0.2403 S12: 0.5460 S13: 0.3380 REMARK 3 S21: -0.6440 S22: 0.1133 S23: 0.2594 REMARK 3 S31: -0.2776 S32: -0.1804 S33: -0.3536 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 127 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7228 16.3642 12.5254 REMARK 3 T TENSOR REMARK 3 T11: 0.0919 T22: 0.1189 REMARK 3 T33: 0.1635 T12: 0.0573 REMARK 3 T13: 0.0540 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 8.7420 L22: 7.1701 REMARK 3 L33: 11.3664 L12: 1.1161 REMARK 3 L13: 3.0142 L23: 3.0295 REMARK 3 S TENSOR REMARK 3 S11: -0.2924 S12: -0.6662 S13: 0.6201 REMARK 3 S21: 0.2937 S22: 0.1499 S23: 0.4131 REMARK 3 S31: -0.5815 S32: -0.2073 S33: 0.1424 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3P75 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MERIDIONALLY-BENT FUSED SILICA REMARK 200 MIRROR WITH PALLADIUM AND REMARK 200 UNCOATED STRIPES. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15431 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ID 3BDC WITH RESIDUE 104 TRUNCATED TO ALA AND REMARK 200 ALL B-FACTORS SET TO 20 A^2. ONLY CONFORMATION A WAS SELECTED REMARK 200 FOR RESIDUES WITH MULTIPLE CONFORMATIONS. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% MPD(W/V), 25 MM CHES, CALCIUM REMARK 280 CHLORIDE, PDTP, PH 9.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 30.39550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 54 -4.61 77.08 REMARK 500 ASN A 138 -103.40 49.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 87.2 REMARK 620 3 THR A 41 O 92.2 76.4 REMARK 620 4 HOH A 162 O 93.3 75.7 151.3 REMARK 620 5 HOH A 163 O 84.6 140.1 65.0 143.7 REMARK 620 6 HOH A 177 O 94.6 149.4 133.8 73.7 70.3 REMARK 620 7 HOH A 191 O 174.1 89.3 82.4 90.4 95.1 90.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 143 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 19 OD2 REMARK 620 2 ASP A 19 OD1 45.4 REMARK 620 3 ASP A 21 OD1 92.3 77.1 REMARK 620 4 THR A 22 OG1 120.2 76.2 84.5 REMARK 620 5 THP A 142 O5P 154.8 158.4 101.7 82.2 REMARK 620 6 HOH A 166 O 83.0 86.8 161.2 82.3 89.7 REMARK 620 7 HOH A 177 O 81.1 121.3 84.3 156.3 79.7 112.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 143 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS AT REMARK 900 CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3H6M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS REMARK 900 V104E AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3C1F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS REMARK 900 V104K AT CRYOGENIC TEMPERATURE DBREF 3P75 A 7 141 UNP P00644 NUC_STAAU 89 223 SEQADV 3P75 A UNP P00644 THR 126 DELETION SEQADV 3P75 A UNP P00644 LYS 127 DELETION SEQADV 3P75 A UNP P00644 HIS 128 DELETION SEQADV 3P75 A UNP P00644 PRO 129 DELETION SEQADV 3P75 A UNP P00644 LYS 130 DELETION SEQADV 3P75 A UNP P00644 LYS 131 DELETION SEQADV 3P75 PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3P75 ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3P75 ASP A 104 UNP P00644 VAL 186 ENGINEERED MUTATION SEQADV 3P75 GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3P75 LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3P75 ALA A 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQRES 1 A 129 LEU HIS LYS GLU PRO ALA THR LEU ILE LYS ALA ILE ASP SEQRES 2 A 129 GLY ASP THR VAL LYS LEU MET TYR LYS GLY GLN PRO MET SEQRES 3 A 129 THR PHE ARG LEU LEU LEU VAL ASP THR PRO GLU PHE ASN SEQRES 4 A 129 GLU LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS SEQRES 5 A 129 MET VAL GLU ASN ALA LYS LYS ILE GLU VAL GLU PHE ASP SEQRES 6 A 129 LYS GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA SEQRES 7 A 129 TYR ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU SEQRES 8 A 129 ASP ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS SEQRES 9 A 129 GLY ASN ASN THR HIS GLU GLN LEU LEU ARG LYS ALA GLU SEQRES 10 A 129 ALA GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER HET CA A 1 1 HET THP A 142 25 HET CA A 143 1 HETNAM CA CALCIUM ION HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE FORMUL 2 CA 2(CA 2+) FORMUL 3 THP C10 H16 N2 O11 P2 FORMUL 5 HOH *54(H2 O) HELIX 1 1 TYR A 54 ALA A 69 1 16 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 LYS A 136 1 16 HELIX 4 4 LEU A 137 SER A 141 5 5 SHEET 1 A 7 LYS A 97 MET A 98 0 SHEET 2 A 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 A 7 ILE A 72 PHE A 76 -1 N GLU A 75 O TYR A 91 SHEET 4 A 7 GLU A 10 ASP A 19 -1 N GLU A 10 O VAL A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O MET A 26 N THR A 13 SHEET 6 A 7 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 7 A 7 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 1 B 2 VAL A 39 ASP A 40 0 SHEET 2 B 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK CA CA A 1 OD2 ASP A 21 1555 1555 2.43 LINK CA CA A 1 OD1 ASP A 40 1555 1555 2.30 LINK CA CA A 1 O THR A 41 1555 1555 2.47 LINK CA CA A 1 O HOH A 162 1555 1555 2.35 LINK CA CA A 1 O HOH A 163 1555 1555 2.59 LINK CA CA A 1 O HOH A 177 1555 1555 2.24 LINK CA CA A 1 O HOH A 191 1555 1555 2.21 LINK OD2 ASP A 19 CA CA A 143 1555 1555 2.80 LINK OD1 ASP A 19 CA CA A 143 1555 1555 2.85 LINK OD1 ASP A 21 CA CA A 143 1555 1555 2.23 LINK OG1ATHR A 22 CA CA A 143 1555 1555 2.67 LINK O5P THP A 142 CA CA A 143 1555 1555 2.32 LINK CA CA A 143 O HOH A 166 1555 1555 2.27 LINK CA CA A 143 O HOH A 177 1555 1555 2.31 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 HOH A 162 SITE 2 AC1 7 HOH A 163 HOH A 177 HOH A 191 SITE 1 AC2 19 ASP A 21 THR A 22 ARG A 35 LEU A 36 SITE 2 AC2 19 ASP A 83 LYS A 84 TYR A 85 ARG A 87 SITE 3 AC2 19 LEU A 89 TYR A 113 LYS A 127 CA A 143 SITE 4 AC2 19 HOH A 147 HOH A 162 HOH A 165 HOH A 169 SITE 5 AC2 19 HOH A 177 HOH A 183 HOH A 188 SITE 1 AC3 6 ASP A 19 ASP A 21 THR A 22 THP A 142 SITE 2 AC3 6 HOH A 166 HOH A 177 CRYST1 31.000 60.791 36.838 90.00 93.45 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.032258 0.000000 0.001944 0.00000 SCALE2 0.000000 0.016450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027195 0.00000